We've been ungrading our dev thor system, and now we see Xref issues. This has been discussed internally, so apologies if I've missed something.

we have tried the following

You need to use daliadmin to delete them + manually expand out the name to the internal representation and delete.

for : "key::salt_coop::rid::meow::father::", it's not clear what the trailing component is, I'm not sure if it's a Scope or a File, or a SuperFile

The internal xpath those would be:

For Scope : /Files/Super[@name="key"]/Scope[@name="salt_coop"]/Scope[@name="rid"]/Scope[@name="meow"]/Scope[@name="father"]/Scope[@name=""]
For File : /Files/Super[@name="key"]/Scope[@name="salt_coop"]/Scope[@name="rid"]/Scope[@name="meow"]/Scope[@name="father"]/File[@name=""]
For SuperFile : /Files/Super[@name="key"]/Scope[@name="salt_coop"]/Scope[@name="rid"]/Scope[@name="meow"]/Scope[@name="father"]/SuperFile[@name=""]

You would remove with, e.g.:
daliadmin <daliip> delete '/Files/Super[@name="key"]/Scope[@name="salt_coop"]/Scope[@name="rid"]/Scope[@name="meow"]/Scope[@name="father"]/Scope[@name=""]'

with the following results

./daliadmin 10.193.64.11 delete '/Files/Super[@name="key"]/Scope[@name="salt_coop"]/Scope[@name="rid"]/Scope[@name="meow"]/Scope[@name="father"]/SuperFile[@name=""]'
ERROR: Could not connect to /Files/Super[@name="key"]/Scope[@name="salt_coop"]/Scope[@name="rid"]/Scope[@name="meow"]/Scope[@name="father"]/SuperFile[@name=""]
Complete at 10:49:02
[root@p-tdalidev01 bin]$ ./daliadmin 10.193.64.11 delete '/Files/Super[@name="key"]/Scope[@name="salt_coop"]'
ERROR: Could not connect to /Files/Super[@name="key"]/Scope[@name="salt_coop"]

most of the time nothing seen in the logs, but we did see once

00002D78 2015-10-20 07:06:54.394 30559 30569 "ERROR: /var/lib/jenkins/workspace/LN-Candidate-withplugins-5.4.2-1/LN/centos-6.4-x86_64/HPCC-Platform/dali/sasha/saxref.cpp(2217) : XREF: : Scope is blank in file name 'key::salt_coop::rid::meow::father::'"

we do see errors in the sasha logs, but they dont seem to be relavent ?

000021B5 2015-11-16 03:27:48.657 113153 113166 "FILEEXPIRY: Deleting scrub::cuem::c100280001::i000240732_b151397001_eexperian_
20150519_030002.txt_postpreprocessor_w20150519-045354_builddata"
000021B6 2015-11-16 03:27:48.730 113153 113166 "ERROR: scrub::cuem::c100280001::i000240732_b151397001_eexperian_20150519_03000
2.txt_postpreprocessor_w20150519-045354_builddata - cause: [ -1: Can't remove scrub::cuem::c100280001::i000240732_b151397001_e
experian_20150519_030002.txt_postpreprocessor_w20150519-045354_builddata: Cannot remove file scrub::cuem::c100280001::i0002407
32_b151397001_eexperian_20150519_030002.txt_postpreprocessor_w20150519-045354_builddata as owned by SuperFile(s): scrub_input:
:cuem::w20150519-110533] "
000021B7 2015-11-16 03:27:48.730 113153 113166 "ERROR: 12: /var/lib/jenkins/workspace/LN-Candidate-withplugins-5.4.2-1/LN/cent
os-6.4-x86_64/HPCC-Platform/dali/sasha/saxref.cpp(2352) : FILEEXPIRY: remove : DFS Exception: 12: Failed to delete file: scrub
::cuem::c100280001::i000240732_b151397001_eexperian_20150519_030002.txt_postpreprocessor_w20150519-045354_builddata - cause: [
-1: Can't remove